Hi,
It's not clear to me exactly what analysis you want to perform. Why
not just specify an atom mask that selects the part of the system you
want to perform analysis on?
The 'center' command does have the ability to center the system on a
structure previously read in by 'reference' - maybe this is what you
want?
-Dan
On Tue, Jun 7, 2016 at 2:43 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Hi List,
>
> I have protein ligand solvated in a box. The ligand is getting displaced in
> the cavity and therefore when I use water-shell command, it shows more
> number of water molecules within 5 A.
>
> Is there a way I can read a reference x y z coordinate in cpptraj and try
> to calculate datasets/analyses around that reference point?
>
> e.g. my reference atom coordinate is 38.30 44.57 60.59 and I want to carry
> out my analyses within 5 A from this coordinate.
>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jun 07 2016 - 08:00:13 PDT
